# ========= [INFO] ==========
# Mut inCB: not accepter mutation in BC
# Mut inMS: 2
# ReadIn  : /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.unmapped.bam
# seq_deb : GACTTAGTC
# seq_fin : TCTCT
# MS_seq : A
# excl : C,G,T
# nom  : A25
# =============================
#
#-------------- Filt ------------------
# condiGrep: GACT.AGTC[ATCGN]+AAAAA[ATCGN]+.CTCT|GACT.AGTC[ATCGN]+AAAAA[ATCGN]+T.TCT|GACT.AGTC[ATCGN]+AAAAA[ATCGN]+TC.CT|GACT.AGTC[ATCGN]+AAAAA[ATCGN]+TCT.T|GACT.AGTC[ATCGN]+AAAAA[ATCGN]+TCTC.|GACTT.GTC[ATCGN]+AAAAA[ATCGN]+.CTCT|GACTT.GTC[ATCGN]+AAAAA[ATCGN]+T.TCT|GACTT.GTC[ATCGN]+AAAAA[ATCGN]+TC.CT|GACTT.GTC[ATCGN]+AAAAA[ATCGN]+TCT.T|GACTT.GTC[ATCGN]+AAAAA[ATCGN]+TCTC.|GACTTA.TC[ATCGN]+AAAAA[ATCGN]+.CTCT|GACTTA.TC[ATCGN]+AAAAA[ATCGN]+T.TCT|GACTTA.TC[ATCGN]+AAAAA[ATCGN]+TC.CT|GACTTA.TC[ATCGN]+AAAAA[ATCGN]+TCT.T|GACTTA.TC[ATCGN]+AAAAA[ATCGN]+TCTC.|GACTTAG.C[ATCGN]+AAAAA[ATCGN]+.CTCT|GACTTAG.C[ATCGN]+AAAAA[ATCGN]+T.TCT|GACTTAG.C[ATCGN]+AAAAA[ATCGN]+TC.CT|GACTTAG.C[ATCGN]+AAAAA[ATCGN]+TCT.T|GACTTAG.C[ATCGN]+AAAAA[ATCGN]+TCTC.|GACTTAGT.[ATCGN]+AAAAA[ATCGN]+.CTCT|GACTTAGT.[ATCGN]+AAAAA[ATCGN]+T.TCT|GACTTAGT.[ATCGN]+AAAAA[ATCGN]+TC.CT|GACTTAGT.[ATCGN]+AAAAA[ATCGN]+TCT.T|GACTTAGT.[ATCGN]+AAAAA[ATCGN]+TCTC.
# condiGrep Rev-Compt: .GAGA[NCGAT]+TTTTT[NCGAT]+.ACTAAGTC|A.AGA[NCGAT]+TTTTT[NCGAT]+.ACTAAGTC|AG.GA[NCGAT]+TTTTT[NCGAT]+.ACTAAGTC|AGA.A[NCGAT]+TTTTT[NCGAT]+.ACTAAGTC|AGAG.[NCGAT]+TTTTT[NCGAT]+.ACTAAGTC|.GAGA[NCGAT]+TTTTT[NCGAT]+G.CTAAGTC|A.AGA[NCGAT]+TTTTT[NCGAT]+G.CTAAGTC|AG.GA[NCGAT]+TTTTT[NCGAT]+G.CTAAGTC|AGA.A[NCGAT]+TTTTT[NCGAT]+G.CTAAGTC|AGAG.[NCGAT]+TTTTT[NCGAT]+G.CTAAGTC|.GAGA[NCGAT]+TTTTT[NCGAT]+GA.TAAGTC|A.AGA[NCGAT]+TTTTT[NCGAT]+GA.TAAGTC|AG.GA[NCGAT]+TTTTT[NCGAT]+GA.TAAGTC|AGA.A[NCGAT]+TTTTT[NCGAT]+GA.TAAGTC|AGAG.[NCGAT]+TTTTT[NCGAT]+GA.TAAGTC|.GAGA[NCGAT]+TTTTT[NCGAT]+GAC.AAGTC|A.AGA[NCGAT]+TTTTT[NCGAT]+GAC.AAGTC|AG.GA[NCGAT]+TTTTT[NCGAT]+GAC.AAGTC|AGA.A[NCGAT]+TTTTT[NCGAT]+GAC.AAGTC|AGAG.[NCGAT]+TTTTT[NCGAT]+GAC.AAGTC|.GAGA[NCGAT]+TTTTT[NCGAT]+GACT.AGTC|A.AGA[NCGAT]+TTTTT[NCGAT]+GACT.AGTC|AG.GA[NCGAT]+TTTTT[NCGAT]+GACT.AGTC|AGA.A[NCGAT]+TTTTT[NCGAT]+GACT.AGTC|AGAG.[NCGAT]+TTTTT[NCGAT]+GACT.AGTC
#--------------------------------------
module load picard/2.8.2
> java -jar /env/gfs/apps/picard/2.8.2/picard.jar SortSam I=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.A25.unmapped.sam O=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.A25.unmapped.sort.sam SORT_ORDER=queryname 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.A25.unmapped.bam ]
